Pepin, WI, is a very small town with a population count of 740 people. There is a motel in town, or a couple little bed and breakfasts, but the best option for overnight stay would be an AirBnB or a nearby larger town.
Just south of Pepin there is a crossing over to Wabasha, MN. An AmericInn is available there, along with some other smaller places to stay. Alternatively, a little farther ways up and across the river from Pepin is Red Wing, MN. This is the largest town near Pepin, so they do have a great assortment of hotels and other places to stay.